+Open data
-Basic information
Entry | Database: PDB / ID: 1e9z | ||||||
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Title | Crystal structure of Helicobacter pylori urease | ||||||
Components |
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Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ha, N.-C. / Oh, S.-T. / Oh, B.-H. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Supramolecular Assembly and Acid Resistance of Helicobacter Pylori Urease Authors: Ha, N.-C. / Oh, S.-T. / Sung, J.Y. / Cha, K.-A. / Hyung Lee, M. / Oh, B.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e9z.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e9z.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 1e9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/1e9z ftp://data.pdbj.org/pub/pdb/validation_reports/e9/1e9z | HTTPS FTP |
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-Related structure data
Related structure data | 1e9yC 1kau C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26571.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14916, urease | ||
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#2: Protein | Mass: 61745.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P69996, urease | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / Method: vapor diffusion, hanging drop / Details: used macroseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 21702 / % possible obs: 95.3 % / Observed criterion σ(I): 1 / Redundancy: 20 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 5.7 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. obs: 23292 / % possible obs: 89.1 % / Num. measured all: 393095 / Rmerge(I) obs: 0.114 |
Reflection shell | *PLUS % possible obs: 75.8 % / Rmerge(I) obs: 0.317 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KAU 1kau Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 40 Å / σ(F): 1 / Rfactor obs: 0.206 / Rfactor Rfree: 0.287 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |